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Monday, June 27, 2011

AMBIT's SMILES depict service

We all know Daylight's Depict service, right? But did you also know the AMBIT version (doi:10.1186/1758-2946-3-18, by IdeaConsult Ltd), which also uses the CDK (Open Source) and Xemistry's CACTVS toolkit (free for academic use)?


3 comments:

  1. I love the information which leaks through in exception tracebacks. Use the SMILES 'Q' and call "http://apps.ideaconsult.net:8080/ambit2/depict/cactvs?search=Q" to see in the traceback "Caused by: http://cactus.nci.nih.gov/chemical/structure/Q/image?width=400&height=200 404 Not Found". The Daylight image traceback says "Caused by: http://www.daylight.com/daycgi/smi2gif?51202373" 500 Internal Server Error".

    In other words, AMBIT does not run Daylight or CACTVS locally but instead proxies (and reformats) information from the primary interface.

    The CDK image is hosted locally, with "Caused by: org.openscience.cdk.exception.InvalidSmilesException: Found element which is not a 'organic subset' element. You must use [Q]." (Interestingly, "C11" is accepted as a valid SMILES, but with a blank image.)

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  2. Yeah, lovely :)

    I also like it for comparing aromaticity models :)

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  3. And now with OpenBabel depiction added

    http://apps.ideaconsult.net:8080/ambit2/depict?search=OC%5BC%40%40H%5D%28O%29%5BC%40%40H%5D%28O%29CO

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